fix: errors in loops section

js2264 · Jan 17, 2024 · 652dc72 · 652dc72
1 parent f575d43
commit 652dc72
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Showing 2 changed files with 5 additions and 16 deletions.
diff --git a/inst/extdata/microC_with-loops.rds b/inst/extdata/microC_with-loops.rds
diff --git a/inst/pages/topological-features.qmd b/inst/pages/topological-features.qmd
@@ -313,20 +313,9 @@ you can import the annotated loops in `R` as follows:
 
 ```{r}
 ## Change the `.tsv` file to the local output file from chromosight
-df <- readr::read_tsv(system.file('extdata', 'chromo.tsv', package = 'OHCA')) 
-loops <- InteractionSet::GInteractions(
-    anchor1 = GenomicRanges::GRanges(
-        df$chrom1, IRanges::IRanges(df$start1, df$end1)
-    ),
-    anchor2 = GenomicRanges::GRanges(
-        df$chrom2, IRanges::IRanges(df$start2, df$end2)
-    ),
-    bin_id1 = df$bin1, 
-    bin_id2 = df$bin2, 
-    score = df$score, 
-    pvalue = df$pvalue, 
-    qvalue = df$qvalue
-)
+loops <- system.file('extdata', 'chromo.tsv', package = 'OHCA') |> 
+    readr::read_tsv() |> 
+    plyinteractions::as_ginteractions(seqnames1 = chrom1, seqnames2 = chrom2)
 
 loops
 ```
@@ -342,8 +331,8 @@ GenomicInteractions::export.bedpe(loops, 'loops.bedpe')
 #### Visualizing chromatin loops
 
 ```{r}
-p <- plotMatrix(
-    refocus(hic, 'chr17:62500001-63500000') |> zoom(5000), 
+plotMatrix(
+    hic, 
     loops = loops,
     limits = c(-4, -1.2),
     caption = FALSE